We have submitted an initiative to NIAID for the development of a library of genetic sequences for critical gene targets for bacterial agents of bioterrorism and other closely related organisms. These gene targets include 16S ribosomal RNA genes and essential housekeeping genes (HKG). As a proof of this approach, we have selected viridans group streptococci because they have long been difficult to identify by traditional phenotypic methods. The viridans streptococci are a group of gram-positive bacteria that constitute part of the resident flora in the human oral cavity and gastrointestinal tract. They can occasionally be found as a cause of transient bacteremia, especially following dental procedures. This group of streptococci has become one of the important causative agents of subacute bacterial endocarditis that can result in serious damage of heart valves. Viridans streptococci are composed of at least 22 species, which are currently divided into 5 subgroups: mitis, anginosus, mutans, salivarius, and bovis. Mitis group streptococci are the most common viridans streptococci responsible for diseases in humans. In the past decades, with the emergence of molecular-based methods, re-classification of viridans streptococci has been evolving and is sometimes confusing. One of the reasons for the ambiguity is that conventional biochemical tests used to identify most of the bacteria isolated in the clinical laboratory often do not provide definitive identification at the species level, and may also misidentify members of this group. A new approach for the identification of bacterial pathogens using 16S rDNA gene sequences has been recently introduced. However, this technique has not been helpful in some closely related organisms that have nearly identical sequences in their 16S genes. We have begun exploring a new set of selected HKG that may show a significant number of DNA base differences among members of the viridans streptococci, specifically the mitis group organisms. In comparison to 16S rDNA sequencing, these HKG may result in a better identification system for these organisms.